Registration Open for Bioc2024
Early registration discount pricing ends May 31!


This is the development version of CellTrails; for the stable release version, see CellTrails.

Reconstruction, visualization and analysis of branching trajectories

Bioconductor version: Development (3.20)

CellTrails is an unsupervised algorithm for the de novo chronological ordering, visualization and analysis of single-cell expression data. CellTrails makes use of a geometrically motivated concept of lower-dimensional manifold learning, which exhibits a multitude of virtues that counteract intrinsic noise of single cell data caused by drop-outs, technical variance, and redundancy of predictive variables. CellTrails enables the reconstruction of branching trajectories and provides an intuitive graphical representation of expression patterns along all branches simultaneously. It allows the user to define and infer the expression dynamics of individual and multiple pathways towards distinct phenotypes.

Author: Daniel Ellwanger [aut, cre, cph]

Maintainer: Daniel Ellwanger < at>

Citation (from within R, enter citation("CellTrails")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

CellTrails: Reconstruction, visualization, and analysis of branching trajectories from single-cell expression data PDF R Script
Reference Manual PDF


biocViews Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, TimeCourse
Version 1.23.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License Artistic-2.0
Depends R (>= 3.5), SingleCellExperiment
Imports BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils
System Requirements
See More
Suggests AnnotationDbi, destiny, RUnit, scater, scran, knitr,, rmarkdown
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CellTrails_1.23.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) CellTrails_1.23.0.tgz
macOS Binary (arm64) CellTrails_1.23.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats